May 21, 2012

Improved adult-derived stem cells have fewer genetic changes

A team of researchers from The Johns Hopkins University and the National Human Genome Research Institute has evaluated the whole genomic sequence of stem cells derived from human bone marrow cells—so-called induced pluripotent stem cells—and found that relatively few genetic changes occur during stem cell conversion by an improved method. The findings, reported in the March issue of Cell Stem Cell, the official journal of the International Society for Stem Cell Research, will be presented at the organization’s annual meeting in June.

“Our results show that human iPS cells accrue genetic changes at about the same rate as any replicating cells, which we don’t feel is a cause for concern,” said Linzhao Cheng, a professor of medicine and oncology in the Johns Hopkins School of Medicine and a member of the Johns Hopkins Institute for Cell Engineering.

Each time a cell divides, it has the chance to make errors and incorporate new genetic changes in its DNA. Some genetic changes can be harmless, Cheng says, but others can lead to changes in cell behavior that may lead to disease and, in the worst case, to cancer.

In the new study, the researchers showed that iPS cells derived from adult bone marrow cells contain random genetic changes that do not specifically predispose the cells to form cancer.

“Little research was done previously to determine the number of DNA changes in stem cells, but because whole-genome sequencing is getting faster and cheaper, we can now more easily assess the genetic stability of these cells derived by various methods and from different tissues,” Cheng said.

Last year, Cheng said, a study published in Nature suggested higher than expected cancer gene mutation rates in iPS cells created from skin samples, raising for many in the field great concerns about the usefulness and safety of the cells. This study analyzed both viral and the improved, nonviral methods to turn on stem cell genes making the iPS cells.

To more thoroughly evaluate the number of genetic changes in iPS cells created by the improved, nonviral method, Cheng’s team first converted human blood-forming cells or their support cells, so-called marrow stromal cells, in adult bone marrow into iPS cells by turning on specific genes and giving those special nutrients. The researchers isolated DNA from—and sequenced—the genome of each type of iPS cells, in comparison with the original cells from which the iPS cells were derived.

Cheng says that they then counted the number of small DNA differences in each cell line compared to the original bone marrow cells. A range of 1,000 to 1,800 changes in the nucleic acid “letters” A, C, T and G occurred across each genome, but only a few changes were found in actual genes—DNA sequences that act as blueprints for our body’s proteins. Such genes make up 2 percent of the genome.

The blood-derived iPS cells contained six and the MSC-derived iPS cells contained 12 DNA letter changes in genes, a finding that led the researchers to conclude that DNA changes in iPS cells are far more likely to occur in the spaces between genes, not in the genes themselves.

Next, the investigators examined the severity of the DNA changes—that is, how likely it would be for a change to disrupt the function of each gene. They found that about half the DNA changes were “silent,” meaning that these altered blueprints wouldn’t change the nucleic acid building code for its corresponding protein or change its function.

For the remaining DNA changes, the researchers guessed that these would, in fact, disrupt the function of the gene by either making the gene inactive or by changing the way the gene works. Since each cell contains two copies of each gene, in many cases the other, normal copy of the gene could compensate for a disrupted gene, Cheng and the team reasoned.

Cheng cautions that disrupting a single gene copy could pose a problem though, for example by shutting down a tumor suppressor gene that prevents cells from malignant growth. However, none of the disrupted genes his team found have been implicated in cancer.

He also noted the absence of overlap in the DNA changes found among the different stem cell lines examined, implying that the changes were random and unlikely to cluster.

Based on these findings, Cheng says, iPS cells don’t seem to pose a heightened cancer risk; but the risk is not zero, the researchers say.

Paul Liu, co–senior author and the deputy scientific director at the National Human Genome Research Institute, said, “We need to sequence more iPS cell lines, including those derived from different cell types and ones using different methods of stem cell conversion, before we have a better picture of mutation rates and spectrums in the iPS cell lines.”

Just because these DNA changes in the stem cells don’t specifically select for cancer formation, he says, doesn’t mean that cancer mutations can’t arise in other iPS cells. Liu adds that to be on the safe side, “it should become a routine procedure to sequence iPS cells before they are used in the clinic.”

Other researchers from Johns Hopkins who contributed to the study are Chunlin Zou, Bin-Kuan Chou, Sarah Dowey and Zhaohui Ye.

Funding for the study was provided by The Johns Hopkins University and the National Institutes of Health.


Related websites

Linzhao Cheng:


Institute for Cell Engineering:


Paul Liu:


NIH Center for Regenerative Medicine: